Opportunities for exploiting the inherent value of protein-rich meat processing co-products, in the context of increased global demand for protein and for sustainable processing systems, are discussed. While direct consumption maybe the most profitable route for some, this approach is influenced greatly by local and cultural traditions. A more profitable and sustainable approach may be found in recognizing this readily available and under-utilised resource can provide high value components, such as proteins, with targeted high value functionality of relevance to a variety of sectors. Applications in food & beverages, petfood biomedical and nutrition arenas are discussed. Utilization of the raw material in its entirety is a necessary underlying principle in this approach to help maintain minimum waste generation. Understanding consumer attitudes to these products, in particular when used in food or beverage systems, is critical in optimizing commercialization strategies.

Following the introduction of legal identifiers of geographic origin within Europe, methods for confirming any such claims are required. Spectroscopic techniques provide a method for rapid and non-destructive data collection and a variety of chemometric approaches have been deployed for their interrogation. In this present study, class-modelling techniques (SIMCA, UNEQ and POTFUN) have been deployed after data compression by principal component analysis for the development of class-models for a set of olive oil and honey. The number of principal components, the confidence level and spectral pre-treatments (1st and 2nd derivative, standard normal variate) were varied, and a strategy for variable selection was tried. Models were evaluated on a separate validation sample set. The outcomes are reported and criteria for selection of the most appropriate models for any given application are discussed.

Diacetyl is a volatile flavour compound that has a characteristic buttery aroma and is widely used in the flavour industry. The aroma of a food plays an important role in food palatability and thus intake. This study investigates the effect of diacetyl on the satiety hormone, glucagon-like peptide (GLP-1), using the enteroendocrine cell line, STC-1. Diacetyl decreased proglucagon mRNA and total GLP-1 from glucose stimulated STC-1 cells. This dampening effect on GLP-1 appears to be mediated by increasing intracellular cAMP levels, increasing synthesis of the G protein coupled receptor, GPR120, and its recruitment to the cell surface. Voltage gated Ca2+ channels, K+ATP channels and the α-gustducin taste pathway do not appear to be involved. These findings demonstrate that components contributing to food palatability suppress GLP-1. This ability of diacetyl to reduce satiety signals may contribute to overconsumption of some palatable foods.

Microorganisms are found throughout nature, thriving in a vast range of environmental conditions. The majority of them are unculturable or difficult to culture by traditional methods. Metagenomics enables the study of all microorganisms, regardless of whether they can be cultured or not, through the analysis of genomic data obtained directly from an environmental sample, providing knowledge of the species present, and allowing the extraction of information regarding the functionality of microbial communities in their natural habitat. Function-based screenings, following the cloning and expression of metagenomic DNA in a heterologous host, can be applied to the discovery of novel proteins of industrial interest encoded by the genes of previously inaccessible microorganisms. Functional metagenomics has considerable potential in the food and pharmaceutical industries, where it can, for instance, aid (i) the identification of enzymes with desirable technological properties, capable of catalyzing novel reactions or replacing existing chemically synthesized catalysts which may be difficult or expensive to produce, and able to work under a wide range of environmental conditions encountered in food and pharmaceutical processing cycles including extreme conditions of temperature, pH, osmolarity, etc; (ii) the discovery of novel bioactives including antimicrobials active against microorganisms of concern both in food and medical settings; (iii) the investigation of industrial and societal issues such as antibiotic resistance development. This review article summarizes the state-of-the-art functional metagenomic methods available and discusses the potential of functional metagenomic approaches to mine as yet unexplored environments to discover novel genes with biotechnological application in the food and pharmaceutical industries.

During routine sampling of bulk raw milk on a dairy farm, the pathogenic bacteria Listeria monocytogenes was found to be a contaminant, at numbers < 100 cfu/ml. A strain with an indistinguishable pulsed-field gel electrophoresis pattern was isolated from the bulk milk two months later. Environmental swabs taken at the dairy environment were negative for the presence of L. monocytogenes, indicating a possible case of excretion of the L. monocytogenes directly into the milk. Milk samples were collected from the individual cows and analysed, resulting in the identification of L. monocytogenes excretion (at 280 cfu/ml) from one of the 4 mammary quarters of one dairy cow out of 180. When the infected cow was isolated from the herd, no L. monocytogenes was detected from the remaining herd. The pulsed-field gel electrophoresis pattern of the strain from the individual cow was indistinguishable from that originally isolated from the bulk milk. The infected cow did not show any clinical signs of disease, nor did the appearance of the milk have any physical abnormalities. Antibiotic treatment of the infected mammary quarter was found to be ineffective. This study shows that there can be risks associated with direct contamination of raw milk with L. monocytogenes.

O'Shea, Norah; Department of Agriculture, Food and the Marine, Ireland(2014-01)

Literature has revealed that “waste” left from the processing of fruit can still
contain a substantial quantity of macro and minor nutrients. The aim of this
thesis was to ascertain the nutritional and structural properties and potential uses
of two fruit by-products [apple pomace (Malus domestica Cv. “Karmijn de
Sonnaville”) and orange pomace (Citrus sinensis L. Cv. “Valencia”)] in glutenfree
bread and extruded snack formulations.
The physicochemical and nutritional properties of the fruit by-products were
initially studied. Apple pomace contained a high level of fibre and pectin. The
isolated pectin was demonstrated to have a high level of methylation which
developed viscous pastes. Orange pomace also had high levels of fibre and
pectin, and it was an abundant source of minerals such as potassium and
magnesium. Orange pomace had a poor gelling ability.
The flour obtained after milling dried orange pomace was used in the formulation
of gluten-free bread with the aid of a response surface design. Due to the fibrous
properties of orange pomace flour, proofing and water addition were also
studied. When added at levels greater than 6%, the loaf volume decreased. The
number of cells per slice also decreased with increasing orange pomace addition.
Inclusion of orange pomace at levels of up to 4% increased crumb softness. An
optimised formulation and proofing time was derived using the optimisation tool;
these consisted of 5.5% orange pomace, 94.6% water inclusion and with 49
minutes proofing. These optimised parameters doubled the total dietary fibre
content of the bread compared to the original control.
The pasting properties, rheology, microstructure and sensory characteristics of
the optimised formulation (batter and bread) were investigated. Pasting results
showed how orange pomace inclusions reduced the final viscosity of the batter,
hence reducing the occurrence of starch gelatinisation. Rheological properties
such as the storage modulus (G') and complex modulus (G*) increased in the
orange pomace batter compared to the control batter. This demonstrates how the
orange pomace as an ingredient improved the robustness of the formulation.
Sensory panellists scored the orange pomace bread comparably to the control
bread.
Milled apple pomace was studied as a potential novel ingredient in an extruded
snack. As extrusion requires the trialling of a number of extruder parameters, a
response surface design was again used to develop an optimised snack. The
parameters studied were apple pomace addition, die head temperature and screw
speed. Screw speed had the most significant impact on extrudate characteristics.
As screw speed increased the favourable extrudate characteristics such as radical
expansion ratio, porosity and specific volume decreased. The inclusion of apple
pomace had a negative effect on extrudate characteristics at levels greater than
8% addition. Including apple pomace reduced the hardness and increased the
crispiness of the snack. Using the optimisation tool, the optimised and validated
formulation and extrusion process contained the following parameters: 7.7%
apple pomace, 150oC die head temperature and a screw speed of 69 rpm.

Background
Lactococcus lactis is among the most widely studied lactic acid bacterial species due to its long history of safe use and economic importance to the dairy industry, where it is exploited as a starter culture in cheese production.
Results
In the current study, we report on the complete sequencing of 16 L. lactis subsp. lactis and L. lactis subsp. cremoris genomes. The chromosomal features of these 16 L. lactis strains in conjunction with 14 completely sequenced, publicly available lactococcal chromosomes were assessed with particular emphasis on discerning the L. lactis subspecies division, evolution and niche adaptation. The deduced pan-genome of L. lactis was found to be closed, indicating that the representative data sets employed for this analysis are sufficient to fully describe the genetic diversity of the taxon.
Conclusions
Niche adaptation appears to play a significant role in governing the genetic content of each L. lactis subspecies, while (differential) genome decay and redundancy in the dairy niche is also highlighted.

Two dimensional Difference Gel Electrophoresis (2-D DIGE) and mass spectrometry were applied to investigate the changes in metabolic proteins that occur over a seven day (day 1, 3 and 7) post mortem ageing period in porcine centrifugal exudate from divergent meat quality phenotypes. The objectives of the research were to enhance our understanding of the phenotype (water holding capacity) and search for biomarkers of this economically significant pork quality attribute. Major changes in protein abundance across nine phenotype-by-time conditions were observed. Proteomic patterns were dominated by post mortem ageing timepoint. Using a machine learning algorithm (l1-regularized logistic regression), a model was derived with the ability to discriminate between high drip and low drip phenotypes using a subset of 25 proteins with an accuracy of 63%. Models discriminating between divergent phenotypes with accuracy of 72% and 73% were also derived comparing respectively, high drip plus intermediate phenotype (considered as one phenotype) versus low drip and comparing low drip plus intermediate phenotype (considered as one phenotype) versus high drip. In all comparisons, the general classes of discriminatory proteins identified include metabolic enzymes, stress response, transport and structural proteins. In this research we have enhanced our understanding of the protein related processes underpinning this phenotype and provided strong data to work toward development of protein biomarkers for water holding capacity.

Phenotypic, chemotaxonomic and genotypic data from 12 strains of Escherichia coli were collected, including carbon source utilisation profiles, ribotypes, sequencing data of the 16S–23S rRNA internal transcribed region (ITS) and Fourier transform-infrared (FT-IR) spectroscopic profiles. The objectives were to compare several identification systems for E. coli and to develop and test a polyphasic taxonomic approach using the four methodologies combined for the sub-typing of O157 and non-O157 E. coli. The nucleotide sequences of the 16S–23S rRNA ITS regions were amplified by polymerase chain reaction (PCR), sequenced and compared with reference data available at the GenBank database using the Basic Local Alignment Search Tool (BLAST) . Additional information comprising the utilisation of carbon sources, riboprint profiles and FT-IR spectra was also collected. The capacity of the methods for the identification and typing of E. coli to species and subspecies levels was evaluated. Data were transformed and integrated to present polyphasic hierarchical clusters and relationships. The study reports the use of an integrated scheme comprising phenotypic, chemotaxonomic and genotypic information (carbon source profile, sequencing of the 16S–23S rRNA ITS, ribotyping and FT-IR spectroscopy) for a more precise characterisation and identification of E. coli. The results showed that identification of E. coli strains by each individual method was limited mainly by the extension and quality of reference databases. On the contrary, the polyphasic approach, whereby heterogeneous taxonomic data were combined and weighted, improved the identification results, gave more consistency to the final clustering and provided additional information on the taxonomic structure and phenotypic behaviour of strains, as shown by the close clustering of strains with similar stress resistance patterns.

Authentication of foods is of importance both to consumers and producers for e.g. confidence in label descriptions and brand protection respectively. The authentication of beers has received limited attention and in most cases only small data sets were analysed. In this study, Fourier-transform infrared attenuated total reflectance (FT-IR ATR) spectroscopy was applied to a set of 267 beers (53 different brands) to confirm claimed identity for samples of a single beer brand based on their spectral profiles. Skewness-adjusted robust principal component analysis (ROBPCA) was deployed to detect outliers in the data. Subsequently, extended canonical variates analysis (ECVA) was used to reduce the dimensionality of the data while simultaneously achieving maximum class separation. Finally, the reduced data were used as inputs to various linear and non-linear classifiers. Work focused on the specific identification of Rochefort 8º (a Trappist beer) and both direct and indirect (using an hierarchical approach) identification strategies were studied. For the classification problems Rochefort versus non-Rochefort, Rochefort 8º versus non-Rochefort 8º and Rochefort 8º versus Rochefort 6º and 10º, correct prediction abilities of 93.8%, 93.3% and 97.3% respectively were achieved.

Adulteration of sulphited strawberry and raspberry purées by apple is a commercial problem. Strawberry (n=31) and raspberry (n=30) purées were prepared from Irish-grown fruit and adulterated at levels of 10-75% w/w using cooking apples. Visible and near infrared transflectance spectra were recorded using a 0.1 mm sample thickness. Classification and quantification models were developed using raw and scatter-corrected and/or derivatised spectral data. Classification as pure strawberry or raspberry was attempted using soft independent modelling of class analogy (SIMCA). The best models used spectral data in the wavelength ranges 400-1098 nm (strawberry) and 750-1098 nm (raspberry) and produced total correct classification rates of 75% (strawberry) and 95% (raspberry). Quantification of apple content was performed using partial least squares (PLS) regression. Lowest predictive errors obtained were 11.3% (raspberry) and 9.0% (strawberry). These results were obtained using spectral data in the wavelength ranges 400-1880 and 1100-1880 nm respectively. These results suggest minimum detection levels of apple in soft fruit purées of approximately 25% and 20% w/w for raspberry and strawberry respectively.

A series of authentic and offal-adulterated beefburger samples was produced. Authentic product (36 samples) comprised either only lean meat and fat (higher quality beefburgers) or lean meat, fat, rusk and water (lower quality product). Offal adulterants comprised heart, liver, kidney and lung. Adulterated formulations (46 samples) were produced using a D-optimal experimental design. Fresh and frozen-then-thawed samples were modelled, separately and in combination, by a classification (partial least squares discriminant analysis) and class-modelling (soft independent modelling of class analogy) approach. With the former, 100% correct classification accuracies were obtained separately for fresh and frozen-then-thawed material. Separate class-models for fresh and frozen-then-thawed samples exhibited high sensitivities (0.94 to 1.0) but lower specificities (0.33 – 0.80 for fresh samples and 0.41 – 0.87 for frozen-then-thawed samples). When fresh and frozen-then-thawed samples were modelled together, sensitivity remained 1.0 but specificity ranged from 0.29 to 0.91. Results indicate a role for this technique in monitoring beefburger compliance to label.

The main aim of this study was to develop a rapid and reliable tool using near infrared (NIR) reflectance spectroscopy to confirm beefburger authenticity in the context of offal (kidney, liver, heart and lung) adulteration. An experimental design was used to develop beefburger formulations to simultaneously maximise the variable space describing offal-adulterated samples and minimise the number of experiments required. Authentic (n = 36) and adulterated (n = 46) beefburger samples were produced using these formulations. Classification models (partial least squares discriminant analysis, PLS1-DA) and class-modelling tools (soft independent modelling of class analogy, SIMCA) were developed using raw and pre-treated NIR reflectance spectra (850-1098 nm wavelength range) to detect authentic and adulterated beefburgers in (1) fresh, (2) frozen-then-thawed and (3) fresh or frozen-then-thawed states. In the case of authentic samples, the best PLS1-DA models achieved 100% correct classification for fresh, frozen-then-thawed and fresh or frozen-then-thawed samples. SIMCA models correctly identified all the fresh samples but not all the frozen-then-thawed and fresh or frozen-then-thawed samples. For the adulterated samples, PLS1-DA models correctly classified 95.5% of fresh, 91.3% of frozen-then-thawed and 88.9% of fresh or frozen-then-thawed beefburgers. SIMCA models exhibited specificity values of 1 for both fresh and frozen-then-thawed samples, 0.99 for fresh or frozen-then-thawed samples; sensitivity values of 1, 0.88 and 0.97 were obtained for fresh, frozen-then-thawed and fresh or frozen-then-thawed products respectively. Quantitative models (PLS1 regression) using both 850-1098 nm and 1100-2498 nm wavelength ranges were developed to quantify (1) offal adulteration and (2) added fat in adulterated beefburgers, both fresh and frozen-then-thawed. Models predicted added fat in fresh samples with acceptable accuracy (RMSECV = 2.0; RPD = 5.9); usefully-accurate predictions of added fat in frozen-then-thawed samples were not obtained nor was prediction of total offal possible in either sample form.

Meat colour is an important criterion in the appeal of meat to consumers at the point of sale. The bright red colour of fresh beef and lamb and the pinkish colour of fresh pork are due to the oxygenation of the myoglobin pigment when the meat is exposed to air. However, exposure to air over several days causes irreversible browning and rejection of the meat by consumers. The gaseous environment in which retail cuts are stored is therefore critical to ensure a good colour over the display life.
Existing packaging systems do not have a sufficiently long storage life for the additional time required for exports from Ireland to the UK or continental Europe. The objective of this project was to develop a bulk packaging system for retail cuts that would have a sufficient shelf life to be used by the Irish industry to export retail ready cuts.
In conclusion, a packaging system has been developed on a laboratory scale which is capable of extending the storage life of some beef cuts, lamb loin chops and pork loin chops. The display life of these after storage is comparable to fresh cuts. In order for this system to be commercialised it would have to be shown to work on a larger scale in a production environment.

Recently, there has been a significant increase in the number of launches of organic bakery products in Ireland. As a result, there is an increased need to identify suitable organic bakery ingredients for use in bread and confectionery formulations. However, only a limited number of scientific studies on the
physical, chemical and functional properties of organic flours and ingredients exist. The effects of commonly-used ingredients in baking, i.e. organic improvers and fats, on the baking characteristics of organic products have not yet been reported and little is known about the influence of approved
additives that may be beneficial to organic baking. Arising from these gaps in the knowledge base on the use of organic flours and ingredients, the objective of this study was to evaluate the chemical,
rheological and baking characteristics of white, wholemeal and confectionery organic flours and to assess the baking potential of organic bakery ingredients, in particular improvers, fats and additives. Ingredients and baked goods were compared to non-organic controls.

In recent years, concern for the environment and consumer dissatisfaction
with conventional food has led to growing interest in organic farming and
food. The demand has also been fuelled by highly-publicised food scares. Food
safety and genetic modification issues have led some consumers to opt for
organic food as a safer alternative.
Recently, there has been a significant increase in the number of launches of
organic bakery products in Ireland. As a result, there is an increased need to
identify suitable organic bakery ingredients for use in bread and confectionery
formulations. However, only a limited number of scientific studies on the
physical, chemical and functional properties of organic flours and ingredients
exist. The effects of commonly-used ingredients in baking, i.e. organic
improvers and fats, on the baking characteristics of organic products have not
yet been reported and little is known about the influence of approved
additives that may be beneficial to organic baking.
Arising from these gaps in the knowledge base on the use of organic flours and
ingredients, the objective of this study was to evaluate the chemical,
rheological and baking characteristics of white, wholemeal and confectionery
organic flours and to assess the baking potential of organic bakery ingredients,
in particular improvers, fats and additives. Ingredients and baked goods were
compared to non-organic controls.

Expansion of the Irish dairy herd has led to more dairy breed male calves being available for beef production. This study investigated the physico-chemical and sensory characteristics of beef from Holstein-Friesian (HF) and Jersey × HF (JEX) young bulls fed pasture grass only or pasture grass plus 2 kg concentrate during their first grazing season and slaughtered at 15, 19 or 22 mo of age. Longissimus thoracis (LT) muscles were collected from 67 carcasses. Postmortem pH, ultimate pH (pHu), meat colour, chemical composition, collagen content and solubility were evaluated. After ageing for 21 d, Warner-Bratzler shear force and cooking loss were determined, and assessments by a trained sensory panel were conducted. Meat from older animals was darker. The pHu, moisture and ash contents decreased, while residual roast beef flavour length increased with age. However, increasing age to slaughter did not negatively influence tenderness. JEX beef had lower cooking loss, was darker and redder, in addition to having higher sensory scores for initial tenderness and fattiness than HF beef. Warner-Bratzler variables were positively correlated with cooking loss and chewiness and were negatively correlated with intramuscular fat (IMF) content, soluble collagen and initial tenderness. In summary, most young dairy bull beef samples were acceptably tender after 21 d of ageing and half of them had acceptable IMF content. Slaughter age affected beef colour, pHu, chemical composition and flavour length. The eating quality of meat from the JEX breed type was considered to be superior to that of the HF breed type. Diet during the first season had no effect on meat quality traits.

The aim of this study was to examine the effect of a single administration of human chorionic gonadotrophin (hCG) during the establishment of the corpus luteum (CL) on progesterone (P4) concentration and pregnancy per artificial insemination (P/AI) in lactating dairy cows. Postpartum spring-calving lactating dairy cows (n = 800; mean ± SD days in milk and parity were 78.5 ± 16.7 and 2.3 ± 0.8, respectively) on 3 farms were enrolled on the study. All cows underwent the same fixed-time AI (FTAI) protocol involving a 7-d progesterone-releasing intravaginal device with gonadotrophin-releasing hormone (GnRH) administration at device insertion, prostaglandin at device removal followed by GnRH 56 h later, and AI 16 h after the second GnRH injection. Cows were blocked on days postpartum, body condition score, and parity and randomly assigned to receive either 3,000 IU of hCG 2 d after FTAI or no further treatment (control). Blood samples were collected on d 7 and 14 postestrus by coccygeal venipuncture on a subset of 204 cows to measure serum P4 concentration, and pregnancy was diagnosed by ultrasonography approximately 30 and 70 d after FTAI. Administration of hCG caused an increase in circulating P4 concentrations compared with the control treatment on d 7 (+22.2%) and d 14 (+25.7%). The P/AI at 30 d after FTAI was affected by treatment, farm, body condition score, and calving to service interval. Overall, administration of hCG decreased P/AI (46.3% vs. 55.1% for the control). Among cows that did not become pregnant following AI, a greater proportion of control cows exhibited a short repeat interval (≤17 d) compared with cows treated with hCG (8.6% vs. 2.8%, respectively). In addition, the percentages of cows pregnant at d 21 (59.6% vs. 52.0%) and d 42 (78.3% vs. 71.9%) were greater in control than in hCG-treated cows. The overall incidence of embryo loss was 10.7% and was not affected by treatment. There was a tendency for an interaction between treatment and CL status at synchronization protocol initiation for both P4 concentration and P/AI. In conclusion, administration of hCG 2 d after FTAI increased circulating P4 concentrations. Unexpectedly, cows treated with hCG had lower fertility; however, this negative effect on fertility was manifested primarily in cows lacking a CL at the onset of the synchronization protocol.

Pulse flours offer nutritional alternatives to wheat flour in the production of baked snacks due to their high protein and fibre levels and low glycaemic index. In this study, broad-bean (Vicia faba), yellow-pea and green-pea (Pisum sativum) flours were each blended with wheat flour at 40% in the formulation of chemically leavened crackers. The effects of flour type and baking time on the physiochemical properties, sensory acceptability, nutritional composition and antioxidant activity of the crackers were observed in comparison with 100% wheat crackers. Broad-bean crackers had the highest protein content and antioxidant activity (13 g per 100 g DM and 38.8 mgAAE per 100 g DM, respectively). Yellow-pea crackers had the highest fibre content (12 g per 100 g DM). Physical dimensions and colour attributes were significantly affected by pulse-flour substitution. Yellow-pea and broad-bean crackers were significantly preferred by consumers compared to the control, demonstrating the potential application of these flours to improve the eating quality and nutritional profile of crackers.

A concentrated form of cell free extract (CFE) derived from attenuated Lactococcus lactis supsb. lactis 303 CFE was encapsulated in liposomes prepared from two different proliposome preparations (Prolipo Duo and Prolipo S) using microfluidization. Entrapment efficiencies of 19.7 % (Prolipo S) and 14.0 % (Prolipo Duo) were achieved and the preparations mixed in the ratio 4 (Prolipo Duo):1 (Prolipo S). Cheddar cheese trials were undertaken evaluating the performance of CFE entrapped in liposomes, empty liposomes and free CFE in comparison to a control cheese without any CFE or liposomes. Identical volumes of liposome and amounts of CFE were used in triplicate trials. The inclusion of liposomes did not adversely impact on cheese composition water activity, or microbiology. Entrapment of CFE in liposomes reduced loss of CFE to the whey. No significant differences were evident in proteolysis or expressed PepX activity during ripening in comparison to the cheeses containing free CFE, empty liposomes or the control, as the liposomes did not degrade during ripening. This result highlights the potential of liposomes to minimize losses of encapsulated enzymes into the whey during cheese production but also highlights the need to optimize the hydrophobicity, zeta potential, size and composition of the liposomes to maximize their use as vectors for enzyme addition in cheese to augment ripening.

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